Mapping the Diversity of Microbial Lignin Catabolism: Experiences from the Elignin Database
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Applied Microbiology and Biotechnology (2019) 103:3979–4002 https://doi.org/10.1007/s00253-019-09692-4 MINI-REVIEW Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database Daniel P. Brink1 & Krithika Ravi2 & Gunnar Lidén2 & Marie F Gorwa-Grauslund1 Received: 22 December 2018 /Revised: 6 February 2019 /Accepted: 9 February 2019 /Published online: 8 April 2019 # The Author(s) 2019 Abstract Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database (www.elignindatabase.com), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings. Keywords Lignin . Database . Aromatic metabolism . Catabolic pathways . Bioconversion . Ecological niche Introduction microbial depolymerization (Ruiz-Dueñas and Martínez 2009). Various types of lignin streams (here called technical Lignin is one of the three main components in lignocellulosic lignins) are produced in high amounts in the pulp and paper biomass and the most abundant terrestrial aromatic macromol- industry and are today primarily used to generate process ecule and is as such a potentially great source of renewable steam and electricity by incineration (Li and Takkellapati aromatic compounds (Holladay et al. 2007). It is found in the 2018; Naqvi et al. 2012). These lignin streams are therefore cell walls of lignocellulosic plants (Fig. 1), where it is a largely untapped resource for sustainable production of plat- intertwined with the other two main polymers (cellulose and form chemicals and have the potential to become a key feed- hemicellulose), and confers structural strength, impermeabili- stock in a future expanded biorefinery concepts (Beckham ty, and water transport in the cell wall (Ayyachamy et al. et al. 2016). 2013). The main characteristic traits of the lignin Microbial lignin degradation in nature has been studied for macropolymer are its highly amorphous structure—caused decades, with the scientific literature stretching back to at least by the high heterogeneity of its aromatic building blocks (in the 1960s and studies on, e.g., Pseudomonas putida (Ornston turn directly depending on the plant species) (Gellerstedt and and Stanier 1966). Due to the high diversity of the lignin Henriksson 2008;LewisandYamamoto1990; Vanholme heteropolymer, the microbial modes of lignin catabolism are et al. 2010)—and its severe recalcitrance to chemical and also diverse (Bugg et al. 2011b; Durante-Rodríguez et al. 2018; Fuchs et al. 2011). Lignin degraders are typically bac- teria and fungi: among the former, the species mostly belong to the Actinobacteria and Proteobacteria phyla (Bugg et al. * Daniel P. Brink [email protected] 2011b;Tianetal.2014); as for the fungi, the common de- graders are of the white rot fungi, filamentous fungi, and yeast taxa (Durham et al. 1984; Guillén et al. 2005; Martins et al. 1 Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden 2015). Furthermore, the lignin recalcitrance often prevents one single species from fully degrading the lignin polymer, 2 Department of Chemical Engineering, Lund University, Lund, Sweden and instead a symbiosis where rot-type fungi and bacteria are 3980 Appl Microbiol Biotechnol (2019) 103:3979–4002 Fig. 1 Schematic representation of the lignin microbial niche. In this enzymatic depolymerization (subgroup 2). There is also some overlap model of the niche, lignin is mineralized by two subgroups: lignolytic between the subgroups, with species capable of both lignolysis and species and aromatic degrading species. Some species degrade or modify aromatic degradation. Yellow circles represent the different origins of lignin to access the hemi-/cellulose on which they grow (subgroup 1), and isolation reported for this niche. The poplar lignin structure was adapted other species catabolize the aromatic lignin fragments that result from the from Vanholme et al. (2010) working together is needed to achieve a complete degradation On the applied side, chemical depolymerization of natural (Cragg et al. 2015; de Boer et al. 2005), thus generating a or technical lignins is required to establish a biotechnological specific niche (Fig. 1) that selects for a small set of microbial value chain from mono- or oligoaromatics. The lignin streams, genera. e.g., from the pulp and paper industry, must be depolymerized Appl Microbiol Biotechnol (2019) 103:3979–4002 3981 to yield mono- and oligomeric aromatic compounds microbial lignin catabolism. A literature survey showed that (Ragauskas et al. 2014; Zakzeski et al. 2010) that are then there have been published databases on lignin biochemistry in fed to suitable microbes (natural or engineered) for bioconver- the past, but they are, at the time of writing, all unavailable sion into value-added products. However, most knowledge on and/or discontinued: FOLy, a database on fungal oxidoreduc- the microbial side of this process comes from natural de- tases for lignin catabolism (Levasseur et al. 2008); LD2L, a graders, and little is currently known about microbial growth database similar in scope as eLignin (Arumugam et al. 2014); and utilization on the cocktail of aromatic compounds found and an NMR database for lignin structures (Ralph et al. 2004), in depolymerized technical lignin. Furthermore, although dif- with the latter not treating microbial catabolism. The objective ferent lignocellulosic feedstocks (e.g., softwood, hardwood, of eLignin is to collect data on strains of microorganisms agricultural residues) are known to contain different amounts (bacteria, yeasts, and fungi) known to degrade and/or catabo- and types of aromatic building blocks (Gellerstedt and lize lignin and lignin-derived aromatic compounds. Henriksson 2008; Ragauskas et al. 2014), it is very challeng- Specifically, the database content includes microorganisms, ing to predict the chemical composition of the mixture substrates, pathways, genes, metabolic reactions, and en- resulting from a depolymerization process, especially for tech- zymes related to the topic (Table 1). So far, its prime focus nical lignins (Abdelaziz et al. 2016). Consequently, it is diffi- has been on collecting data on microbial diversity and cult to a priori select a suitable microbial host until chemical intracellular events; however, the database can later be ex- analysis has been performed on the depolymerized (low mo- panded with extracellular enzymes and reactions (such as lecular weight) lignin stream. laccases and peroxidases), as these play an important role in The literature on microbial lignin catabolism is vast and microbial degradation of native lignin and can be applied for combines fundamental microbiology and applied studies that enzymatic depolymerzation of technical lignins (Bourbonnais have in particular seen a surge in popularity during the last et al. 1995; Pardo et al. 2018;Zhaoetal.2016). decade. However, there has been little effort yet to facilitate an In practice, the data in eLignin is retrieved from scientific overview of the large amount of publications in this field, literature (peer-reviewed articles, reviews, and books), manu- especially regarding intracellular microbial events. For this ally curated and supplemented with links to relevant entries in reason, we have created a new database named The eLignin other well-established biological and chemical databases (e.g., Microbial Database (www.elignindatabase.com)for GenBank (Benson et al. 2012), KEGG (Kanehisa and Goto collection of data from scientific literature on the catabolism 2000), PubChem (Kim et al. 2015), and ChEBI (Hastings of lignin and lignin-derived aromatic compound by microor- et al. 2012)). The initial dataset was collected by performing ganisms. The eLignin database was launched online in a systematic literature review according to the Kitchenham March 2017 and aims to bring together the bibliome of this protocol (Kitchenham 2004), where 561 articles (title, ab- field in one self-contained searchable platform, and thus fill a stract, and keywords) were screened and analyzed for their gap presently not covered by other online biological data- inclusion in the database bibliome. Since the eLignin dataset bases, as well as to demonstrate the high diversity of this originates from scientific literature, users are encouraged to microbial niche (Fig. 1). As the database primarily focuses read the primary references for any data of interest, since there on intracellular conversion steps, information on extracellular will be aspects of the data that are not indexed or reviewed by enzymes with lignolytic activities are currently not covered eLignin (such as experimental conditions).